rs7780294

Positions:

• chr7-128736608-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.107 in 152,190 control chromosomes in the GnomAD database, including 1,918 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.11 (1918 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.33

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.568 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.107 AC: 16283 AN: 152072 Hom.: 1916 Cov.: 33

Gnomad AFR AF: 0.0424

Gnomad AMI AF: 0.0835

Gnomad AMR AF: 0.249

Gnomad ASJ AF: 0.0519

Gnomad EAS AF: 0.586

Gnomad SAS AF: 0.184

Gnomad FIN AF: 0.107

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.0762

Gnomad OTH AF: 0.0986

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.107 AC: 16296 AN: 152190 Hom.: 1918 Cov.: 33 AF XY: 0.114 AC XY: 8513 AN XY: 74416

Gnomad4 AFR AF: 0.0423

Gnomad4 AMR AF: 0.250

Gnomad4 ASJ AF: 0.0519

Gnomad4 EAS AF: 0.586

Gnomad4 SAS AF: 0.184

Gnomad4 FIN AF: 0.107

Gnomad4 NFE AF: 0.0762

Gnomad4 OTH AF: 0.0999

Alfa AF: 0.0906 Hom.: 1397

Bravo AF: 0.119

Asia WGS AF: 0.356 AC: 1236 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.24
DANN	Benign	0.64

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs7780294; hg19: chr7-128376662;